def populate_trimming(self):
title = "Trimming (raw data)"
df = self._get_df("get_trimming_percent")
self.df['Trimmed'] = df.copy()
self.df['Trimmed'].columns = ['name', 'url', 'Trimmed_reads_(%)']
cb = CanvasBar(df, title, "trimming", xlabel="Percentage")
self.jinja['canvas'] += cb.to_html()
self.jinja['sections'].append(self._get_div("trimming", title))
def populate_gc_samples(self):
title = "GC content (raw)"
df = self._get_df("get_gc_content_samples")
self.df['GC_raw'] = df.copy()
self.df['GC_raw'].columns = ['name', 'url', 'GC_raw_(%)']
cb = CanvasBar(df, title, "populate_gc_samples", xlabel="Percentage")
self.jinja['canvas'] += cb.to_html(options={"maxrange":100})
self.jinja['sections'].append(self._get_div("populate_gc_samples",title))
def populate_phix(self):
title = "Phix content"
df = self._get_df("get_phix_percent")
self.df['Phix'] = df.copy()
self.df['Phix'].columns = ['name', 'url', 'Phix_content_(%)']
cb = CanvasBar(df, title, "phix", xlabel="Percentage")
self.jinja['canvas'] += cb.to_html()
self.jinja['sections'].append(self._get_div("phix", title))
def populate_adapters(self):
title = "Adapters content"
df = self._get_df("get_adapters_percent")
self.df['Adapters'] = df.copy()
self.df['Adapters'].columns = ['name', 'url', 'Adapters_content_(%)']
cb = CanvasBar(df, "Adapters content", "adapters", xlabel="Percentage")
self.jinja['canvas'] += cb.to_html()
self.jinja['sections'].append(self._get_div("adapters", title))
def populate_mean_quality(self):
title = "Mean quality (raw data)"
df = self._get_df("get_mean_quality_samples")
self.df['Mean_quality_raw'] = df.copy()
self.df['Mean_quality_raw'].columns = ['name', 'url', 'Mean_quality_raw']
cb = CanvasBar(df, title, "mean_quality", xlabel="mean quality")
self.jinja['canvas'] += cb.to_html(options={'maxrange':40})
self.jinja['sections'].append(self._get_div("mean_quality", title))
def populate_nreads_raw(self):
title = "Number of reads"
df = self._get_df("get_nreads_raw")
self.df['N_raw'] = df.copy()
self.df['N_raw'].columns = ['name', 'url', 'N_raw']
cb = CanvasBar(df, "Number of reads (raw data)", "nreads_raw",
xlabel="Number of reads")
self.jinja['canvas'] += cb.to_html()
self.jinja['sections'].append(self._get_div("nreads_raw",title))
def populate_gc_samples(self):
title = "GC content (raw)"
df = self._get_df("get_gc_content_samples")
self.df['GC_raw'] = df.copy()
self.df['GC_raw'].rename({'value': 'GC_raw_(%)'}, axis=1, inplace=True)
cb = CanvasBar(df, title, "populate_gc_samples", xlabel="Percentage")
self.jinja['canvas'] += cb.to_html(options={"maxrange": 100})
self.jinja['sections'].append(
self._get_div("populate_gc_samples", title))
def populate_trimming(self):
title = "Trimming (raw data)"
df = self._get_df("get_trimming_percent")
self.df['Trimmed'] = df.copy()
self.df['Trimmed'].rename({'value': 'Trimmed_reads_(%)'},
axis=1,
inplace=True)
cb = CanvasBar(df, title, "trimming", xlabel="Percentage")
self.jinja['canvas'] += cb.to_html()
self.jinja['sections'].append(self._get_div("trimming", title))
def populate_phix(self):
title = "Phix content"
df = self._get_df("get_phix_percent")
self.df['Phix'] = df.copy()
self.df['Phix'].rename({'value': 'Phix_content_(%)'},
inplace=True,
axis=1)
cb = CanvasBar(df, title, "phix", xlabel="Percentage")
self.jinja['canvas'] += cb.to_html()
self.jinja['sections'].append(self._get_div("phix", title))
def populate_mean_quality(self):
title = "Mean quality (raw data)"
df = self._get_df("get_mean_quality_samples")
self.df['Mean_quality_raw'] = df.copy()
self.df['Mean_quality_raw'].rename({'value': 'Mean_quality_raw'},
axis=1,
inplace=True)
cb = CanvasBar(df, title, "mean_quality", xlabel="mean quality")
self.jinja['canvas'] += cb.to_html(options={'maxrange': 40})
self.jinja['sections'].append(self._get_div("mean_quality", title))
def populate_adapters(self):
title = "Adapters content"
df = self._get_df("get_adapters_percent")
self.df['Adapters'] = df.copy()
self.df['Adapters'].rename({'value': 'Adapters_content_(%)'},
axis=1,
inplace=True)
cb = CanvasBar(df, "Adapters content", "adapters", xlabel="Percentage")
self.jinja['canvas'] += cb.to_html()
self.jinja['sections'].append(self._get_div("adapters", title))
def populate_nreads_raw(self):
title = "Number of reads"
df = self._get_df("get_nreads_raw")
self.df['N_raw'] = df.copy()
self.df['N_raw'].rename({'value': 'N_raw'}, axis=1, inplace=True)
cb = CanvasBar(df,
"Number of reads (raw data)",
"nreads_raw",
xlabel="Number of reads")
self.jinja['canvas'] += cb.to_html()
self.jinja['sections'].append(self._get_div("nreads_raw", title))